Variant report

Variant	rs2015554
Chromosome Location	chr12:494274-494275
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:494061..497561-chr12:499622..502914,3	K562	blood:
2	chr12:486794..489246-chr12:492841..495214,2	K562	blood:
3	chr12:490753..496037-chr12:496468..499221,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120647	Chromatin interaction
ENSG00000073614	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10431355	0.84[AMR][1000 genomes]
rs10735021	0.84[AMR][1000 genomes]
rs10774137	0.81[AMR][1000 genomes]
rs10774152	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774153	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774169	0.85[ASN][1000 genomes]
rs10848814	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10848815	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10848838	0.81[AMR][1000 genomes]
rs10848845	0.81[AMR][1000 genomes]
rs10848849	0.81[AMR][1000 genomes]
rs10848879	0.84[AMR][1000 genomes]
rs12311569	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581260	0.84[ASN][1000 genomes]
rs16929744	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16929783	0.91[ASN][1000 genomes]
rs2007537	0.90[ASN][1000 genomes]
rs2079785	0.80[AMR][1000 genomes]
rs2284334	0.81[ASN][1000 genomes]
rs2300131	0.92[ASN][1000 genomes]
rs2300133	0.81[AMR][1000 genomes]
rs2300134	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2369276	0.84[AMR][1000 genomes]
rs3213750	0.81[ASN][1000 genomes]
rs3753156	0.84[ASN][1000 genomes]
rs3759371	0.84[AMR][1000 genomes]
rs3782852	0.81[AMR][1000 genomes]
rs4980877	0.81[ASN][1000 genomes]
rs4980881	0.83[ASN][1000 genomes]
rs4980886	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6489448	0.84[AMR][1000 genomes]
rs6489449	0.84[AMR][1000 genomes]
rs6489454	0.84[AMR][1000 genomes]
rs6489458	0.81[AMR][1000 genomes]
rs6489471	0.84[AMR][1000 genomes]
rs6489477	0.81[AMR][1000 genomes]
rs6489478	0.81[AMR][1000 genomes]
rs7132763	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7132845	0.94[ASN][1000 genomes]
rs7134353	0.81[ASN][1000 genomes]
rs7134608	0.84[AMR][1000 genomes]
rs7136957	0.84[AMR][1000 genomes]
rs7138890	0.84[AMR][1000 genomes]
rs7138958	0.90[ASN][1000 genomes]
rs7138981	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs715228	0.81[AMR][1000 genomes]
rs715229	0.81[AMR][1000 genomes]
rs715230	0.81[AMR][1000 genomes]
rs720128	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7298995	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303180	0.81[ASN][1000 genomes]
rs7312065	0.84[AMR][1000 genomes]
rs7315852	0.81[ASN][1000 genomes]
rs7316660	0.84[AMR][1000 genomes]
rs764614	0.80[AMR][1000 genomes]
rs7953137	0.84[AMR][1000 genomes]
rs7963793	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7965303	0.84[AMR][1000 genomes]
rs887311	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9669094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9739950	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv1050781	chr12:321353-783899	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1040849	chr12:321619-771493	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv541322	chr12:321619-771493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1035679	chr12:321619-781558	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
14	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
15	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	esv2757484	chr12:335010-543206	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
18	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
19	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv1050646	chr12:362398-658665	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
21	nsv541326	chr12:362398-658665	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
22	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
23	nsv898565	chr12:428131-564185	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	nsv1052201	chr12:429128-515675	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv541328	chr12:429128-515675	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv442250	chr12:432808-543847	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
27	esv2756520	chr12:433151-543206	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
28	nsv1050226	chr12:441032-743195	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
29	nsv1035222	chr12:449993-515675	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
31	nsv949226	chr12:493900-814882	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2015554	JARID1A	Cis_1M	lymphoblastoid	RTeQTL
rs2015554	CCDC77	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:474800-495200	Weak transcription	Fetal Heart	heart
2	chr12:475200-496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:484000-494400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:484200-494400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:484400-494400	Strong transcription	Liver	Liver
6	chr12:484400-494800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:484400-494800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:484400-494800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:484400-494800	Strong transcription	Primary B cells from cord blood	blood
10	chr12:484400-494800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:484400-495000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:484400-495000	Strong transcription	Fetal Thymus	thymus
13	chr12:484400-495200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:484600-494400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:484600-495000	Strong transcription	A549	lung
16	chr12:485400-495000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr12:485400-495600	Weak transcription	Psoas Muscle	Psoas
18	chr12:485800-495400	Strong transcription	HSMM	muscle
19	chr12:486000-497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:486400-497200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:487000-496200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:487200-494600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:487400-494400	Strong transcription	Fetal Intestine Small	intestine
24	chr12:487600-495000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:487600-495000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:487600-495000	Weak transcription	Fetal Brain Male	brain
27	chr12:487600-495400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:487800-494800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:488000-496600	Weak transcription	Right Ventricle	heart
30	chr12:488200-495600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:488400-495200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:488600-495400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:489400-495000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:489400-495000	Weak transcription	Stomach Mucosa	stomach
35	chr12:491800-494400	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:492000-494800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr12:492000-495000	Strong transcription	NHDF-Ad	bronchial
38	chr12:492000-495600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:492200-494400	Strong transcription	Hela-S3	cervix
40	chr12:492400-494800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr12:492800-495000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:492800-497000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:493400-494800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:493400-494800	Weak transcription	Small Intestine	intestine
45	chr12:493400-495200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:493400-495600	Genic enhancers	Dnd41	blood
47	chr12:493400-496800	Weak transcription	Colonic Mucosa	Colon
48	chr12:493600-494800	Weak transcription	Fetal Kidney	kidney
49	chr12:493600-495000	Weak transcription	Fetal Brain Female	brain
50	chr12:493600-495000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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